NPM1

NPM1
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 2LLH, 2P1B, 2VXD
Identifiers
Aliases	NPM1, B23, NPM, nucleophosmin (nucleolar phosphoprotein B23, numatrin), nucleophosmin, nucleophosmin 1
External IDs	OMIM: 164040; MGI: 106184; HomoloGene: 81697; GeneCards: NPM1; OMA:NPM1 - orthologs
Gene location (Human) Chr. Chromosome 5 (human) Band 5q35.1 Start 171,387,116 bp End 171,411,810 bp
Gene location (Mouse) Chr. Chromosome 11 (mouse) Band 11|11 A4 Start 33,102,287 bp End 33,113,206 bp
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in Achilles tendon left ovary ventricular zone right ovary canal of the cervix body of uterus ganglionic eminence body of pancreas right uterine tube ectocervix Top expressed in tail of embryo epiblast genital tubercle morula embryo primary oocyte zygote secondary oocyte embryo blastocyst More reference expression data BioGPS More reference expression data
Gene ontology Molecular function ribosomal large subunit binding protein homodimerization activity ribosomal small subunit binding unfolded protein binding transcription coactivator activity protein kinase inhibitor activity histone binding Tat protein binding NF-kappaB binding protein binding RNA binding protein heterodimerization activity nucleic acid binding protein kinase binding transcription factor binding rRNA binding protein N-terminus binding chromatin binding Cellular component cytoplasm membrane focal adhesion spindle pole centrosome nucleoplasm microtubule organizing center nucleolus cytoskeleton nucleus protein-DNA complex granular component centrosome cytosol large ribosomal subunit small ribosomal subunit nuclear speck protein-containing complex ribonucleoprotein complex Biological process centrosome cycle regulation of eIF2 alpha phosphorylation by dsRNA positive regulation of cell cycle G2/M phase transition negative regulation of centrosome duplication regulation of centriole replication response to stress positive regulation of translation CENP-A containing chromatin assembly positive regulation of transcription, DNA-templated positive regulation of NF-kappaB transcription factor activity protein complex oligomerization negative regulation of protein kinase activity by regulation of protein phosphorylation regulation of endodeoxyribonuclease activity regulation of endoribonuclease activity ribosome assembly intracellular protein transport DNA repair signal transduction negative regulation of cell population proliferation nucleosome assembly viral process DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest regulation of transcription by RNA polymerase II cellular response to UV ribosomal large subunit export from nucleus ribosomal small subunit export from nucleus rRNA export from nucleus cell volume homeostasis nucleocytoplasmic transport protein localization positive regulation of cell population proliferation posttranscriptional regulation of gene expression negative regulation of gene expression regulation of centrosome duplication positive regulation of centrosome duplication cell growth positive regulation of cellular biosynthetic process positive regulation of protein ubiquitination regulation of protein stability ribosomal large subunit biogenesis ribosomal small subunit biogenesis negative regulation of apoptotic process regulation of DNA damage response, signal transduction by p53 class mediator positive regulation of protein kinase activity positive regulation of transcription by RNA polymerase II negative regulation of mRNA splicing, via spliceosome protein stabilization protein homooligomerization regulation of cell cycle positive regulation of protein localization to nucleolus chromatin remodeling regulation of mRNA stability involved in cellular response to UV Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 4869 18148 Ensembl ENSG00000181163 ENSMUSG00000057113 UniProt P06748 Q61937 RefSeq (mRNA) NM_001037738 NM_002520 NM_199185 NM_001355006 NM_001355009 NM_001355007 NM_001355010 NM_001252260 NM_001252261 NM_008722 RefSeq (protein) NP_001032827 NP_002511 NP_954654 NP_001341935 NP_001341938 NP_001341936 NP_001341939 NP_001239189 NP_001239190 NP_032748 Location (UCSC) Chr 5: 171.39 – 171.41 Mb Chr 11: 33.1 – 33.11 Mb PubMed search
Wikidata
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Nucleophosmin (NPM), also known as nucleolar phosphoprotein B23 or numatrin, is a protein that in humans is encoded by the NPM1 gene.

Gene

In humans, the NPM1 gene is located on the long arm of chromosome 5 (5q35). The gene spans 23 kb and contains 12 exons. Three transcript variants have been described. The longest isoform (294 amino acids long), encoded by transcript variant 1, is the major and the most well studied isoform of Nucleophosmin. Transcript variant 2 is produced by skipping an in-frame exon (exon 8) to produce an isoform that is 265 amino acids long. However, this isoform is not well characterized and its functions and expression pattern is not well understood. Transcript variant 3 is produced by using an alternate exon (exon 10) which results in an isoform 259 amino acids long with a different C-terminal sequence. The isoforms 1 and 3 of human NPM1 are B23.1 and B23.2 respectively in rat. The isoform 1 is localized to the nucleolus as is reported for rat B23.1 whereas the isoform 3 (B23.2) is nucleoplasmic or cytoplasmic in localization and is expressed at relatively lower levels as compared to isoform 1 in normal rat tissues and in HeLa cells. Both isoforms 1 and 3 have been shown to stimulate the replication of adenoviral DNA complexed with viral basic proteins.

Function

NPM1 is associated with nucleolar ribonucleoprotein structures and binds single-stranded and double-stranded nucleic acids, but it binds preferentially G-quadruplex forming nucleic acids. It is involved in the biogenesis of ribosomes and may assist small basic proteins in their transport to the nucleolus. Its regulation through SUMOylation (by SENP3 and SENP5) is another facet of the protein's regulation and cellular functions.

It is located in the nucleolus, but it can be translocated to the nucleoplasm in case of serum starvation or treatment with anticancer drugs. The protein was identified as a phosphoprotein. However, later other post-translational modifications for NPM1 were identified including acetylation and SUMOylation.

Nucleophosmin has multiple functions:

1. Histone chaperones
2. Ribosome biogenesis and transport
3. Genomic stability and DNA repair
4. Endoribonuclease activity
5. Centrosome duplication during cell cycle
6. Regulation of ARF-p53 tumor suppressor pathway
7. RNA helix destabilizing activity
8. Inhibition of caspase-activated DNase
9. Prevents apoptosis when located in nucleolus

Molecular and histone chaperone

NPM1 functions as a molecular chaperone for several proteins. Both the N-terminal hydrophobic core domain and acidic stretches are important for this activity. Furthermore, oligomerization of NPM1 has been shown to be necessary for maximum chaperone activity. NPM1 has been predicted to play a role in preventing protein aggregation in the densely packed nucleolus especially during ribosome biogenesis. NPM1 shows characteristic properties of molecular chaperones such as a) preventing temperature dependent and independent aggregation of proteins, b) preserving enzyme activities during thermal denaturation of several different proteins, c) promoting the renaturation of previously denatured proteins, d) preferentially binding to denatured proteins, and exposing hydrophobic regions during interaction with other proteins. NPM1 can bind to ATP, yet, its chaperoning function does not require ATP hydrolysis or the presence of ATP.

NPM1 is known to associate with pre-ribosomal particles and other nucleolar proteins. Since ribosomal proteins tend to be insoluble under physiological conditions, NPM1 presumably binds to ribosomal proteins in the nucleolus, prevent them from aggregation and promote their assembly into the ribosomal subunits. Similarly, certain viral proteins such as HIV-1 Rev that are insoluble under physiological conditions, bind to NPM1 which prevents their aggregation and allows their accumulation in the nucleus/nucleolus thereby promoting viral particle assembly. Further, since NPM1 can shuttle between the nucleus and the cytoplasm by virtue of its NES and NLS, it could help in co-translational folding of client proteins in the cytoplasm and promote their entry into the nucleus/nucleolus.

NPM1 is a highly acidic protein and can bind to histones directly because of their basic nature. NPM1 binding to histones is retained even at a salt concentration of 0.5 M KCl suggesting a strong binding with the help of electrostatic interactions. However, electrostatic interactions alone are not responsible for binding to histones as is suggested by the NPM1 core crystal structure. NPM1 directly binds to core histones H2B, H3 and H4 and can bind to H2A only in the presence of the H2A-H2B dimer or the core histone octamer. It can assemble nucleosomes in vitro and can decondense sperm chromatin similar to nucleoplasmin. NPM1 histone chaperone activity has been suggested to be involved in nucleosome disassembly during transcription resulting in activation of transcription. It is also presumed to function as a histone chaperone in the nucleolus. Depletion of NPM1 or overexpression of a mutant NPM1 lacking histone chaperone activity leads to a decrease in rDNA transcription. It can also bind to linker histone H1 and promote its assembly or disassembly from chromatin.

Ribosome biogenesis

NPM1 is a molecular chaperone. It was also observed to associate with preribosomes, hence it was initially thought that NPM1 is a ribosome assembly factor or a ribosome chaperone. Other characteristic properties that suggest NPM1 role in ribosome biogenesis are nucleolar localization, ability to shuttle between the nucleus and cytoplasm, ability to bind to nucleic acid and to transport pre-ribosomal particles. NPM1 also has an intrinsic ribonuclease activity that cleaves a specific site in the ITS2 (Internal transcribed spacer 2) of the pre-5.8S rRNA. Knockdown of NPM1 leads to changes in the profiles of ribosomes. (Grisendi et al., 2005) Degradation of NPM1 induced by ARF leads to defects in the processing of pre-ribosomal RNA from the 32S precursor rRNA to the 28S rRNA species (Itahana et al., 2003). Moreover, blocking the NPM1 nucleo-cytoplasmic shuttling inhibits ribosome subunit export resulting in a decrease in the cell growth rate showing that NPM1 exports pre-ribosomes (Maggi et al., 2008). Furthermore, NPM1 interacts with a number of ribosomal proteins including RPL5 (Yu et al., 2006), RPS9 (Lindström and Zhang, 2008) and RPL23 (Wanzel et al., 2008). NPM3 was shown to bind to NPM1 and negatively regulate ribosome biogenesis whereas an NPM1 binding defective mutant of NPM3 did not have any effect on ribosome biogenesis (Huang et al., 2001). Interestingly, NPM1 isoform 3 that does not have a nucleic acid binding domain also inhibits ribosome biogenesis. All these findings suggest an important role of NPM1 in ribosome biogenesis.

Most cancer cells have enlarged nucleoli and the aberrant overexpression of NPM1 has been correlated well with the increased ribosome biogenesis in highly proliferating cells. Thus NPM1 by controlling ribosome biogenesis could control the proliferative rate of cells. NPM1 knockout mouse embryos survive upto mid-gestation (9.5dpc-12.5dpc) (Colombo et al., 2005; Grisendi et al., 2005), whereas, knockout of pescadillo, a protein involved in ribosome biogenesis, leads to death of the embryos at morula stages (2.5 dpc) (Lerch-Gaggl et al., 2002). This suggests that either NPM1 may not be essential for ribosome biogenesis, as other proteins could have overlapping functions with NPM1 or there could be other factors such as ribosome storage in oocytes that could have compensated for the loss of NPM1 in NPM1 null embryos (Grisendi et al., 2006).

Role in Transcriptional regulation

NPM1 has been shown to be an important co-activator for RNA Polymerase II driven transcription. Acetylation of NPM1 enhances this activity through increased histone binding and chaperone activity. Intriguingly acetylated NPM1 (AcNPM1) is a distinct pool localized in the nucleoplasm in contrast to the nucleolar localization of unmodified and phosphorylated NPM1. Genome-wide profiling of AcNPM1 occupancy by ChIP-sequencing reveals that it localizes to the transcription start site of many gene promoters and is co-occupied with RNA Polymerase II.

Clinical significance

The NPM1 gene is up-regulated, mutated and chromosomally translocated in many tumor types. Chromosomal aberrations involving NPM1 were found in patients with non-Hodgkin lymphoma, acute promyelocytic leukemia, myelodysplastic syndrome, and acute myelogenous leukemia. Heterozygous mice for NPM1 are vulnerable to tumor development. In solid tumors NPM1 is frequently found overexpressed, and it is thought that NPM1 could promote tumor growth by inactivation of the tumor suppressor p53/ARF pathway; on the contrary, when expressed at low levels, NPM1 could suppress tumor growth by the inhibition of centrosome duplication.

Of high importance is NPM involvement in acute myelogenous leukemia, where a mutated protein lacking a folded C-terminal domain (NPM1c+) has been found in the cytoplasm in patients. This aberrant localization has been linked to the development of the disease, and is associated with improved clinical outcomes. Strategies against this subtype of acute myelogenous leukemia include the refolding of the C-terminal domain using pharmalogical chaperones and the displacement of the protein from nucleolus to nucleoplasm, which has been linked to apoptotic mechanisms. It has also been shown that in the context of clonal hematopoiesis of undetermined significance harboring a DNMT3A mutation, subsequent NPM1 mutations drive progression into overt myeloproliferative neoplasm.

In addition, NPM1 is overexpressed in many solid tumors including gastric, colon, breast, ovary, bladder, oral, thyroid, brain, liver, prostate cancer and multiple myeloma. NPM1 overexpression correlates well with the clinical features of hepatocellular carcinoma suggesting that NPM1 overexpression could serve as a diagnostic marker for hepatocellular carcinoma. NPM1 overexpression and hyperacetylation progresses according to the increasing grade of tumor in OSCC. NPM1 overexpression also correlates well with recurrence and progression of bladder cancer to advanced stages. NPM1 overexpression is associated with acquired oestrogen-independence in human breast cancer cells (Skaar et al., 1998). Moreover, NPM1 is a direct transcriptional target of oncogenic transcription factor c-myc (Zeller et al., 2001). The ability of NPM1 to suppress apoptosis and promote DNA repair might be responsible for the survival of tumor cells where NPM1 is overexpressed. All these studies suggest that NPM1 overexpression promotes tumor development and hence could function as a proto-oncogene.

Discovery

NPM1 was first discovered as a nucleolar phosphoprotein in rat liver cells and Novikoff hepatoma ascites cells. It was named B23 as it was the 23rd spot in the B section of the 2-D gel where spots were numbered in the order of decreasing mobility. It was named numatrin independently by another group as it was found to be tightly associated with the nuclear matrix and its expression was induced upon mitogenic signals in human B lymphocytes. At around the same time, the Xenopus NO38 was discovered and was found to be homologous to Xenopus Nucleoplasmin and rat B23.

Structure

The NPM1 protein can be divided into several domains with sequence motifs that are conserved across nucleoplasmin family and have important and distinct functions. The N-terminal core domain, the acidic stretches, basic domain and the aromatic nucleic acid domain make up the NPM1 protein. Further, sequence motifs such as the nuclear export signals (NES), nuclear localization signals (NLS) and the nucleolar localization signals (NoLS) are critical for the localization of NPM1 to the nucleolus as well as its nucleo-cytoplasmic shuttling required for its diverse array of functions.

The N-terminal domain also known as the core domain (residues 1-119 of human NPM1) is the most conserved domain among the NPM family proteins. This domain folds into a distinct structure that is protease resistant and is responsible for the oligomerization and chaperone activity of these proteins. It contains several hydrophobic residues that are highly conserved (~80%) among NPM proteins. The crystal structure of NPM1 core domain (residues 9-122) shows that this domain folds into an eight stranded β-barrel with jelly roll topology forming a wedge shaped hydrophobic core that fits snugly to form a pentamer through hydrophobic interactions between the monomeric subunits. Two pentameric complexes align in a head to head fashion to form the decameric structure. A comparison between the crystal structure of human NPM1 and that of the core domains of Xenopus NO38, Xenopus Nucleoplasmin and Drosophila Nucleoplasmin like protein (dNLP) show that both the monomeric and pentameric structures are highly similar among all the NPM family proteins. The human NPM1 core domain (residues 15-118) shares a sequence identity of 80%, 51% and 29% with Xenopus NO38, Nucleoplasmin and Drosophila NLP cores respectively. All of them form the same β barrel structure with jelly roll topology.

NPM1 was speculated to be a hexamer under native conditions since it was found to have a molecular weight of 230–255 kDa calculated by gel filtration chromatography and sedimentation analyses. However, the crystal structure of the NPM1 core clearly shows that it is a pentamer. The pentamer-pentamer interface consists of several water molecules involved in hydrogen bonding between the two pentamers. Moreover, ten charge based interactions between the Asp of the highly conserved AKDE loop and Lys82 give additional stability. Comparison of dNLP and Nucleoplasmin structures has revealed that formation of the decamer might be facilitated by histone binding. The H2A-H2B dimer may bind to the lateral surface of the NPM1 decamer. Furthermore, comparison of the crystal structures of human NPM1 and Xenopus NO38 reveals structural plasticity in the pentamer-pentamer interface. When one of the pentamers of human NPM1 and Xenopus NO38 are superimposed, there is a large rotational offset (~20°) between the other pentamers. Further, the direction of the rotational offsets are opposite for human NPM1 and Xenopus NO38 when compared to Xenopus Nucleoplasmin core structure. The significance of this structural plasticity is not well understood, however, it may have a significance in the chaperone function of NPM1.

Interactions

NPM1 has been shown to interact with

• AKT1,
• BARD1,
• BRCA1, and
• nucleolin.
• linker histone H1.

Nucleophosmin has multiple binding partners:

1. rRNA
2. HIV Rev and Rex peptide
3. p53 tumor suppressor
4. ARF tumor suppressor
5. MDM2 (mouse double minute 2, ubiquitin ligase)
6. Ribosome protein S9
7. Phosphatidylinositol 3,4,5-triphosphate (PIP3)
8. Exportin-1 (CRM1, chromosome region maintenance)
9. Nucleolin/C23
10. Transcription target of myc oncogene

Further reading

• Yun C, Wang Y, Mukhopadhyay D, Backlund P, Kolli N, Yergey A, et al. (November 2008). "Nucleolar protein B23/nucleophosmin regulates the vertebrate SUMO pathway through SENP3 and SENP5 proteases". The Journal of Cell Biology. 183 (4): 589–595. doi:10.1083/jcb.200807185. PMC 2582899. PMID 19015314.
• Haindl M, Harasim T, Eick D, Muller S (March 2008). "The nucleolar SUMO-specific protease SENP3 reverses SUMO modification of nucleophosmin and is required for rRNA processing". EMBO Reports. 9 (3): 273–279. doi:10.1038/embor.2008.3. PMC 2267381. PMID 18259216.
• Li L, Li HS, Pauza CD, Bukrinsky M, Zhao RY (2006). "Roles of HIV-1 auxiliary proteins in viral pathogenesis and host-pathogen interactions". Cell Research. 15 (11–12): 923–934. doi:10.1038/sj.cr.7290370. PMID 16354571. S2CID 24253878.
• Gjerset RA (September 2006). "DNA damage, p14ARF, nucleophosmin (NPM/B23), and cancer". Journal of Molecular Histology. 37 (5–7): 239–251. doi:10.1007/s10735-006-9040-y. PMID 16855788. S2CID 24017618.
• Chen W, Rassidakis GZ, Medeiros LJ (November 2006). "Nucleophosmin gene mutations in acute myeloid leukemia". Archives of Pathology & Laboratory Medicine. 130 (11): 1687–1692. doi:10.5858/2006-130-1687-NGMIAM. PMID 17076533.
• Falini B, Nicoletti I, Bolli N, Martelli MP, Liso A, Gorello P, et al. (April 2007). "Translocations and mutations involving the nucleophosmin (NPM1) gene in lymphomas and leukemias". Haematologica. 92 (4): 519–532. doi:10.3324/haematol.11007. hdl:2434/424144. PMID 17488663.
• Fankhauser C, Izaurralde E, Adachi Y, Wingfield P, Laemmli UK (May 1991). "Specific complex of human immunodeficiency virus type 1 rev and nucleolar B23 proteins: dissociation by the Rev response element". Molecular and Cellular Biology. 11 (5): 2567–2575. doi:10.1128/MCB.11.5.2567. PMC 360026. PMID 2017166.
• Venkatesh LK, Mohammed S, Chinnadurai G (May 1990). "Functional domains of the HIV-1 rev gene required for trans-regulation and subcellular localization". Virology. 176 (1): 39–47. doi:10.1016/0042-6822(90)90228-J. PMID 2109912.
• Cochrane AW, Perkins A, Rosen CA (February 1990). "Identification of sequences important in the nucleolar localization of human immunodeficiency virus Rev: relevance of nucleolar localization to function". Journal of Virology. 64 (2): 881–885. doi:10.1128/JVI.64.2.881-885.1990. PMC 249184. PMID 2404140.
• Chan PK, Chan WY, Yung BY, Cook RG, Aldrich MB, Ku D, et al. (October 1986). "Amino acid sequence of a specific antigenic peptide of protein B23". The Journal of Biological Chemistry. 261 (30): 14335–14341. doi:10.1016/S0021-9258(18)67023-1. PMID 2429957.
• Zhang XX, Thomis DC, Samuel CE (October 1989). "Isolation and characterization of a molecular cDNA clone of a human mRNA from interferon-treated cells encoding nucleolar protein B23, numatrin". Biochemical and Biophysical Research Communications. 164 (1): 176–184. doi:10.1016/0006-291X(89)91699-9. PMID 2478125.
• Hale TK, Mansfield BC (December 1989). "Nucleotide sequence of a cDNA clone representing a third allele of human protein B23". Nucleic Acids Research. 17 (23): 10112. PMC 335249. PMID 2602120.
• Chan WY, Liu QR, Borjigin J, Busch H, Rennert OM, Tease LA, Chan PK (February 1989). "Characterization of the cDNA encoding human nucleophosmin and studies of its role in normal and abnormal growth". Biochemistry. 28 (3): 1033–1039. doi:10.1021/bi00429a017. PMID 2713355.
• Li XZ, McNeilage LJ, Whittingham S (August 1989). "The nucleotide sequence of a human cDNA encoding the highly conserved nucleolar phosphoprotein B23". Biochemical and Biophysical Research Communications. 163 (1): 72–78. doi:10.1016/0006-291X(89)92100-1. PMID 2775293.
• Chan PK, Aldrich M, Cook RG, Busch H (February 1986). "Amino acid sequence of protein B23 phosphorylation site". The Journal of Biological Chemistry. 261 (4): 1868–1872. doi:10.1016/S0021-9258(18)67023-1. PMID 3944116.
• Bocker T, Bittinger A, Wieland W, Buettner R, Fauser G, Hofstaedter F, Rüschoff J (April 1995). "In vitro and ex vivo expression of nucleolar proteins B23 and p120 in benign and malignant epithelial lesions of the prostate". Modern Pathology. 8 (3): 226–231. PMID 7542384.
• Dundr M, Leno GH, Hammarskjöld ML, Rekosh D, Helga-Maria C, Olson MO (August 1995). "The roles of nucleolar structure and function in the subcellular location of the HIV-1 Rev protein". Journal of Cell Science. 108 ( Pt 8) (8): 2811–2823. doi:10.1242/jcs.108.8.2811. PMID 7593322.
• Miyazaki Y, Takamatsu T, Nosaka T, Fujita S, Martin TE, Hatanaka M (July 1995). "The cytotoxicity of human immunodeficiency virus type 1 Rev: implications for its interaction with the nucleolar protein B23". Experimental Cell Research. 219 (1): 93–101. doi:10.1006/excr.1995.1209. PMID 7628555.
• Szebeni A, Herrera JE, Olson MO (June 1995). "Interaction of nucleolar protein B23 with peptides related to nuclear localization signals". Biochemistry. 34 (25): 8037–8042. doi:10.1021/bi00025a009. PMID 7794916.
• Kato S, Sekine S, Oh SW, Kim NS, Umezawa Y, Abe N, et al. (December 1994). "Construction of a human full-length cDNA bank". Gene. 150 (2): 243–250. doi:10.1016/0378-1119(94)90433-2. PMID 7821789.
• Marasco WA, Szilvay AM, Kalland KH, Helland DG, Reyes HM, Walter RJ (1995). "Spatial association of HIV-1 tat protein and the nucleolar transport protein B23 in stably transfected Jurkat T-cells". Archives of Virology. 139 (1–2): 133–154. doi:10.1007/BF01309460. PMID 7826206. S2CID 24710329.
• Valdez BC, Perlaky L, Henning D, Saijo Y, Chan PK, Busch H (September 1994). "Identification of the nuclear and nucleolar localization signals of the protein p120. Interaction with translocation protein B23". The Journal of Biological Chemistry. 269 (38): 23776–23783. doi:10.1016/S0021-9258(17)31583-1. PMID 8089149.